/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.transfer;

import com.github.lindenb.jbwa.jni.ShortRead;
import org.ncic.bioinfo.sparkseq.compress.BaseCompressTools;
import org.ncic.bioinfo.sparkseq.compress.QualityCompressTools;
import org.ncic.bioinfo.sparkseq.data.basic.FastqPairRecord;
import org.ncic.bioinfo.sparkseq.data.basic.FastqRecord;

/**
 * Author: wbc
 */
public class FastqRecord2ShortReadTransfer {

    public static ShortRead transfer(FastqRecord record) {
        String readName = record.descriptionLine();
        byte[] seq = record.sequence();
        byte[] qual = record.quality();
        if(record.compressFlag()){
            qual = QualityCompressTools.deCompressQual(qual);
            seq = BaseCompressTools.decompressBase(seq, qual);
        }
        return new ShortRead(readName, seq, qual);
    }

    public static ShortRead transferRead1(FastqPairRecord record) {
        String readName = record.descriptionLine();
        byte[] seq = record.sequence1();
        byte[] qual = record.quality1();
        if (record.compressFlag()) {
            qual = QualityCompressTools.deCompressQual(qual);
            seq = BaseCompressTools.decompressBase(seq, qual);
        }
        return new ShortRead(readName, seq, qual);
    }

    public static ShortRead transferRead2(FastqPairRecord record) {
        String readName = record.descriptionLine();
        byte[] seq = record.sequence2();
        byte[] qual = record.quality2();
        if (record.compressFlag()) {
            qual = QualityCompressTools.deCompressQual(qual);
            seq = BaseCompressTools.decompressBase(seq, qual);
        }
        return new ShortRead(readName, seq, qual);
    }
}
